Uncovering novel biological processes and pathogenic mechanisms for glaucoma

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Project Summary/Abstract Glaucoma is a leading cause of irreversible vision loss affecting 60 million people world-wide. Despite this, prevention and treatment of glaucoma are limited. Primary open angle glaucoma (POAG), the most common form, is characterized by progressive retinal ganglion cell death leading to optic neuropathy, often caused by elevated intraocular pressure (IOP). The long-term goals of the proposed research are to identify genomic regions that affect gene expression in glaucoma-relevant eye tissues, and in combination with large-scale human genetic association studies, to uncover novel causal genes and key biological processes that can lead to glaucoma, which may serve as effective drug targets for novel therapies. Genome-wide association studies (GWAS) have led to the discovery of over 20 genomic loci associated with POAG and over 100 loci associated with IOP, however extracting biological insights from these genetic associations has been challenging, largely due to the fact that the associated variants lie in noncoding regions. Furthermore, much of the heritability of glaucoma has yet to be detected. The Genotype-Tissue Expression (GTEx) project has shown that genetic variants associated with gene expression variation (eQTLs) substantially contribute to disease risk, however GTEx does not contain data for ocular tissues. The working hypothesis of the proposed research, supported by our preliminary results, is that hundreds of regulatory effects will contribute to the pathogenicity of glaucoma and will explain much of its heritability, and that the affected genes will cluster in disease-relevant biological processes. We thus propose in Aim 1, to create a high-quality map of the transcriptome and open chromatin regions (indicative of transcriptional activity), and to identify genetic variants associated with gene expression (eQTLs) and alternative splicing (sQTLs) in four key pathogenic tissues for glaucoma: outflow pathway (trabecular meshwork and Schlemm’s canal), ciliary body, optic nerve, and macular retina, collected from 100 postmortem donors. We will use RNA-seq, ATAC-seq, and whole genome sequencing on bulk tissue and we will further identify cell type-specific eQTLs and sQTLs using cell type-specific gene expression profiles from single cell RNA-seq studies that are available to us. In Aim 2, we will apply novel computational and statistical methods that integrate data from Aim 1 with GWAS data of high or normal-tension glaucoma and several risk factor traits, with the goal of identifying new genetic associations, and the underlying causal genes, pathways, and pathogenic cell types for glaucoma. To broaden the impact of our work, we will build a web-based platform for sharing, browsing, and inspecting gene expression and genetic regulation data from the different eye tissues in relation to genetic associations with glaucoma and other complex eye traits (Aim 3). The proposed research is expected to significantly improve our understanding of the pathophysiology of glaucoma, uncover novel genetic risk factors, and open new avenues for therapeutic development. Our genomics eye resource will also be valuable for studying the molecular causes of other eye diseases, such as retinal degeneration diseases, and for tissue-targeted gene therapy design.